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WO2003054197A2 - Bibliotheque de genes structuraux modifies ou de particules modifiees par des capsides utiles pour l'identification de clones viraux par tropisme cellulaire desire - Google Patents

Bibliotheque de genes structuraux modifies ou de particules modifiees par des capsides utiles pour l'identification de clones viraux par tropisme cellulaire desire Download PDF

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WO2003054197A2
WO2003054197A2 PCT/EP2002/014750 EP0214750W WO03054197A2 WO 2003054197 A2 WO2003054197 A2 WO 2003054197A2 EP 0214750 W EP0214750 W EP 0214750W WO 03054197 A2 WO03054197 A2 WO 03054197A2
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Prior art keywords
nucleic acid
virions
cell
library
gene
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German (de)
English (en)
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WO2003054197A3 (fr
Inventor
Luca Perabo
Hildegard BÜNING
Jörg ENSSLE
Martin Ried
Michael Hallek
Nadja Huttner
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Medigene AG
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Medigene AG
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Priority to ES02787962.6T priority Critical patent/ES2467156T3/es
Priority to US10/498,163 priority patent/US20050106558A1/en
Priority to EP02787962.6A priority patent/EP1456383B1/fr
Priority to CA2468882A priority patent/CA2468882C/fr
Priority to JP2003554898A priority patent/JP2005512569A/ja
Priority to AU2002352261A priority patent/AU2002352261B2/en
Publication of WO2003054197A2 publication Critical patent/WO2003054197A2/fr
Publication of WO2003054197A3 publication Critical patent/WO2003054197A3/fr
Anticipated expiration legal-status Critical
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C12N15/86—Viral vectors
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/20—Antivirals for DNA viruses
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2750/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssDNA viruses
    • C12N2750/00011—Details
    • C12N2750/14011—Parvoviridae
    • C12N2750/14111—Dependovirus, e.g. adenoassociated viruses
    • C12N2750/14122—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2750/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssDNA viruses
    • C12N2750/00011—Details
    • C12N2750/14011—Parvoviridae
    • C12N2750/14111—Dependovirus, e.g. adenoassociated viruses
    • C12N2750/14141—Use of virus, viral particle or viral elements as a vector
    • C12N2750/14143—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector

Definitions

  • the present invention relates to libraries containing modified parvovirus cap genes useful for the identification of parvovirus capsids able to transduce predefined cell types as well as to methods for the production thereof.
  • the control of the tropism of the vector represents a critical concern in the development of viral gene transfer systems for gene therapy: to allow efficient transfer of the therapeutic genes to the target cells and to avoid transduction of undesired cell types.
  • Efforts to achieve these goals led to the description of several approaches aimed to provide virions with the ability to interact with spe- cific cellular receptors.
  • One of these approaches includes the coupling of viral particles to receptor-binding molecules, which results in retargeted vectors with improved specificity.
  • a big disadvantage of this technology is however that these retargeting molecules could detach from the capsids, restoring the natural tropism of the virions.
  • a different approach consists in the genetic modification of the viral capsid or envelope proteins by site directed mutagenesis, mostly by insertional mutagenesis.
  • Parvoviruses and especially the Adeno-associated virus have received increasing attention as a vector for gene therapy because of their non-pafhogenicity, their low immunogenicity, and their ability to infect both dividing and non- dividing cells and to facilitate long term expression of the therapeutic genes. Furthermore, AAV is able to integrate site specifically into the genome of the infected cell without impairing any cellular function.
  • a great disadvantage of the use of parvoviruses and other viruses in gene therapy is the fact that these viruses are only able to efficiently transduce specific cell types, while other cell types are resistant against a parvovirus infection.
  • AAV2 is only able to transduce cells having heparan sulfate proteoglycan (HSPG) on their surface (Girod A. et al.(1999) Nature Medicine 5-9, 1052-56).
  • HSPG heparan sulfate proteoglycan
  • an RGD motif containing peptide (a portion of the laminin fragment PI)
  • AAV immunoassisted virus
  • the B16F10 cells express an integrin and are, due to the lack of expression of heparan sulfate proteoglycans at the outer cellular membrane, resistant to infection with wtAAV2.
  • the present invention relates therefore in a first subject matter to a method for the production of a library of nucleic acids comprising a multiplicity of expressible structural genes from at least one eukaryotic virus, comprising the steps of:
  • nucleic acids each encoding at least one structural gene from a eukaryotic virus and comprising a suitable packaging sequence
  • the expression "structural gene” relates to a gene encoding one or more proteins, preferably structural proteins of a viral capsid either of a non-enveloped or an enveloped virus or to gene encoding one or more proteins, preferably structural proteins of a viral shell of enveloped viruses.
  • the invention further relates to a library of nucleic acids comprising a multiplicity of expressible structural genes from at least one eukaryotic virus, obtainable by the above method.
  • the library of the invention contains a multiplicity of nucleic acids with different structural genes which may be expressed in order to form infectious viral particles with a tropism for different cell types. Given a certain cell type, it is therefore possible to screen the library for mutant viruses, especially parvoviruses which are able to infect that specific cell type.
  • capsid protein means a protein encoded by a cap gene
  • functional capsid protein means a capsid protein of a virus able to infect at least one host cell.
  • the capsid protein may be VP1, VP2 or VP3, for other parvoviruses names and numbers of the capsid proteins may differ.
  • the term "packaging sequence” means a cis-acting nucleic acid sequence that mediates the packaging of a nucleic acid into a viral capsid.
  • the so called “inverted terminal repeats” (ITRs) that are located at the 5 ' and 3 ' end of the linear viral genome have this function.
  • the structural genes are from an enveloped virus such as a retrovirus, lentivirus, herpes virus, e.g. HSVl, HSV2, EBV, Varizella zoster virus, human herpes virus 1, 2, 3, 4, 7 or 8.
  • the structural genes are cap genes, preferably from a non-enveloped virus such as parvovirus or adeno virus. In this case, the cap genes encode for one or more capsid proteins
  • cap gene relates to a gene encoding one or more proteins of a viral capsid either of a non-enveloped or an enveloped virus.
  • the cap genes are from a parvovirus selected from the group consisting of Adeno-associated Virus (AAV), Canine Parvovirus (CPV), MVM, B19, HI, AAAV (Avian AAV) or GPV (goose parvovirus).
  • AAV Adeno-associated Virus
  • CPV Canine Parvovirus
  • MVM MVM
  • B19 HI
  • AAAV Elimavirus
  • GPV goose parvovirus
  • the cap genes are from an AAV, e.g. AAV1, AAV2, AAV3, AAV4, AAV5 or AAV6.
  • the library obtainable by the method of the invention has a multiplicity of viral mutants that is greater than 10 , preferably greater than 10 5 , especially greater than 10 6 and, in another preferred embodiment, a multi- plicity of expressible structural genes, preferably cap genes that is greater than 10 , preferably greater that 10 , especially greater that 10 .
  • the set of nucleic acids is derived from one nucleic acid.
  • the library is constituted of a multiplicity of nucleic acids which are, apart from the insert, almost identical.
  • the set of nucleic acids may be derived from different nucleic acids encoding structural genes. In this case, it is preferred that the nucleic acids are derived from one virus.
  • one insert (1) is inserted into the structural gene.
  • more than one inserts (1) are inserted.
  • the insertion may, dependent on the insertion site, lead to an amino acid insertion in one or more structural proteins, preferably capsid proteins, e. g. VP1, VP2 and/or VP3 in the case of AAV.
  • capsid proteins e. g. VP1, VP2 and/or VP3 in the case of AAV.
  • parvovirus capsid proteins are encoded by only one cap gene by overlapping reading frames.
  • a sequence of the structural gene is removed by inserting insert (1).
  • the removed sequence comprises or is part of an insert (2) inserted into the structural gene before step (a).
  • the method further comprises an initial step, wherein the structural gene is modified to render the structural gene non-functional.
  • This can be achieved i.e. by inserting insert (2).
  • insert (2) By a replacement of insert (2) with insert (1) in step a) of the method, potentially functional structural genes will be formed.
  • this additional step leads to a reduced number of parvovirus virions that have a capsid built from viral capsid proteins not en- compassing insert (1) and therefore enables the formation of libraries with high titers.
  • insert (2) prevents the formation of a functional structural protein, preferably a capsid protein, preferably by con- taining a stop codon. Furthermore, insert (2) may shift the open reading frame or may introduce additional amino acids which disturb the formation of functional capsids or their infection biology at any further step.
  • insert (1) and/ or insert (2) contains further at least two restriction sites, preferably one at its 3 '-end and one at its 5' -end.
  • insert (2) is at least partially replaced by insert (1), whereby the prevention of the formation of functional capsids is - at least for some capsids - abolished, in a preferred embodiment by removing the stop codon.
  • the number of nucleotides of insert (1) and/or insert (2), preferably of insert (1) and insert (2) is three or a multiple of three.
  • insert (1) is inserted at a region of the cap gene encoding amino acids on the surface of the capsid protein.
  • the virus is AAV2 and insert (1) is inserted after a nucleic acid corresponding to a site within the first amino terminal amino acids 1 to 50, or corresponding to amino acid positions 261, 381, 447, 534, 573, and/or 587 of the capsid protein VP1, preferably corresponding to amino acid position 447 or 587.
  • insert (1) is inserted in nucleic acids corre- sponding to the adjacent 5 amino acid of the above indicated insertion sites, as these amino acid stretches represent loops of the AAV2-capsid and therefore are located on the surface of the capsid protein. It is possible for the person skilled in the art to identify corresponding loops and insertion site for other parvoviruses by known techniques such as sequence alignment, three-dimensional structure analy- sis, protein folding, hydrophobicity analysis (Girod A et al, 1999 supra).
  • Especially preferred insertion sites are within the stretches consisting of amino acids (aa) i) aa 261 -270, especially aa 269, ii) aa 324-331, iii) aa 380-383, especially aa 381, iv) aa 447-460, especially aa 447 and 451 -460, v) aa 484-503, preferably aa 484-499, especially aa 484, 487 or aa 494-499, vi) aa 507-514, especially aa 507, 509 or 514, vii) aa 527-534, especially 527-529, 532 or 534, viii) aa-548-556, ix) aa 572-575, especially 573, x) aa 581-595, especially 585, 587, 588 or 594.
  • the numbering of amino acids relates to the VP1 protein of AAV2 (Girod A et al, 1999 supra).
  • Stretches v) and vi) are especially preferred.
  • insert (1) inserted into the nucleic acid my be identical for all structural genes where an insert (1) is inserted. However, it is preferred that insert (1) is different or at least potentially different for all structural genes where an insert (1) is inserted.
  • insert (1) is randomly or partially randomly generated. This means that the insert (1) introduced in one structural gene is potentially different from the insert (1) inserted in another structural gene, although it is theoretically possible that two inserts (1) are identical.
  • the codons NNN, NNB or NNK are used.
  • the inserted nucleic acid sequences may be partially randomly generated, especially using codons with one, two or three fixed nucleo- tides.
  • the length of such insertions may be preferably at least 3 nucleotides, preferably at least 9, especially at least 18 nucleotides.
  • insert (1) may contain, in addition to the randomly or partially randomly generated sequences, a further stretch of at least one codon upstream and/or downstream of the randomized or partially randomized nucleic acid sequences, preferably of one or two or three codons coding for Ala, Gly, Leu, He, Asp- and/or- Arg, -especially -an insertion of three codons for Ala-upstream-and two codons for Ala downstream of the randomized or partially randomized nucleic acid sequences.
  • insert (1) does not contain any stop codons. This can be achieved by not having an A or G at the third position of the codons of insert
  • the library obtainable by the method of the invention may have the features as defined below for the library of nucleic acids comprising a multiplicity of expressible structural genes from at least one eukaryotic virus.
  • this invention relates to a library of nucleic acids comprising a multiplicity of expressible structural genes, preferably cap genes, from an eukaryotic virus, preferably of a parvovirus, especially dependoviruses such as Adeno-associated virus or a canine parvovirus (CPV) as well as autonomous parvoviruses such as HI, MVM (minute virus of mice) or B19, AAAV or GPV.
  • dependoviruses such as Adeno-associated virus or a canine parvovirus (CPV)
  • CPV canine parvovirus
  • autonomous parvoviruses such as HI, MVM (minute virus of mice) or B19, AAAV or GPV.
  • Said library of nucleic acids may encode eucaryotic viruses with a multiplicity of modifications of the virion's external structure and/or of the corresponding (en- coding) genetic information.
  • the library has a preferred multiplicity of viral mu- tants that is greater than 10 , preferably greater that 10 , especially greater that 10 6 .
  • the library of nucleic acids has a multiplicity of ex- pressible structural genes, preferably cap genes that is greater than 10 2 , preferably greater that 10 5 , especially greater that 10 6 .
  • the library may be in the form of a linear nucleic acid, a plasmid, a viral particle or a viral vector, e.g. a recombinant AAV, Adenovirus or Herpes Simplex Virus vector.
  • the nucleic acid may additionally comprise packaging sequences (e.g. AAV ITRs) and expressible genes providing necessary functions for replication and packaging of virions (e.g. non-structural genes for parvoviruses such as AAV rep gene).
  • packaging sequences e.g. AAV ITRs
  • expressible genes providing necessary functions for replication and packaging of virions e.g. non-structural genes for parvoviruses such as AAV rep gene.
  • sequences, genes or functions may be provided in cis (meaning on the same construct as the packaging sequences and the capsid proteins encoding genes) or in trans (meaning on a different construct) However, the packaging sequences must be provided in cis.
  • the nucleic acid is DNA.
  • the cap gene as well as packaging sequences such as ITRs and genes providing necessary functions for replication and packaging of virions, such as the rep gene are derived from parvoviruses, preferably from de- pendoviruses such as AAV or CPV, especially from one of the AAV serotypes from the group comprising AAV1, AAV2, AAV3, AAV4, AAV5 and AAV6 or from autonomous parvoviruses such as HI, MVM, B19, AAAV or GPV.
  • parvoviruses preferably from de- pendoviruses such as AAV or CPV, especially from one of the AAV serotypes from the group comprising AAV1, AAV2, AAV3, AAV4, AAV5 and AAV6 or from autonomous parvoviruses such as HI, MVM, B19, AAAV or GPV.
  • Another preferred embodiment relates to a library, wherein the AAV cap gene is derived from the AAV cap gene encoded in plasmid pWT99oen (see Fig. 1 and Example 1).
  • the multiplicity of nucleic acid sequences are inserted into at least one site of the structural gene, preferably the cap gene, wherein the number of inserted nucleotides is three or a multiple of three. According to preferred embodiments, the multiplicity of nucleic acid sequences are inserted into one, two or three sites of the structural gene, preferably the cap gene.
  • a second or further insert (1) may contain non randomized codons for amino acid stretches of choice. This has the advantage that one can simultaneously screen for expressible structural genes with a wanted property by inserting a randomized insert (1) and one or more further inserts (1) at different sites to change the properties of such an expressible structural gene.
  • a randomized insert (1) with the insertion of further fixed inserts (1) preferably at known or presumed epitopes to change the immunogenicity of the vector.
  • a randomized insert (1) and screening for a vector with an increased infectivity or specificity for a specific cell type (rAAV- 587/Mec, example 7) or by inserting a fixed insert (rAAV-587/L14, example 7) one can abolish or reduce the neutralizing effects of antibodies.
  • the invention can also be used to make or screen for vectors that have a reduced binding to antibodies (monoclonal or polyclonal antibodies/sera) and/or to have the ability to escape neutralizing antibodies and therefore are able to escape from an immune response in a patient.
  • antibodies monoclonal or polyclonal antibodies/sera
  • the length of such insertions is at least 3 nucleotides, preferably at least 9, especially at -least T 8 nucleotides.
  • the inserted nucleic acid sequences may have been inserted using standard restriction endonucleases, recombination systems, e.g. the gateway or the cre/lox recombination system or polymerase chain reaction techniques, e.g. using degen- erated primers.
  • the inserted nucleic acid sequences shall lead to an insertion of amino acids into at least one viral capsid protein, i.e. in the case of AAV into VP1, VP2 and/or VP3 structural protein, preferably at a site that is located on the surface of the cap- sid of the virion.
  • the inserted nucleic acid sequences may be inserted at any site within the first amino terminal amino acids 1 to 50 of VP1, after corresponding amino acid positions 261, 381, 447, 534, 573, and/or 587 of VP1, preferably after amino acid po- sition 447 or 587.
  • the numbering of the amino acids relates to the position within VP1. For the avoidance of doubt, corresponding sites of VP2 and VP3 of course have a different number.
  • the inserted nucleic acid sequences may be inserted after a nucleic acid conesponding to any site within the first amino terminal amino acids 1 to 50 of VP1, or corresponding to amino acid positions 261, 381, 447, 534, 573, and/or 587 of VP1, preferably to amino acid position 447 or 587.
  • the numbering of the amino acids relates to the position within VP1. For the avoidance of doubt, corresponding sites of VP2 and VP3 of course have a differ- ent number.
  • insert (1) is inserted in nucleic acids corresponding to the adjacent 5 amino acid of the above indicated insertion sites, as these amino acid stretches represent loops of the AAV2-capsid and therefore are located on the surface of the capsid protein. It is possible for the person skilled in - the art to identify corresponding loops and insertion site for other parvoviruses by known techniques such as sequence alignment, three-dimensional structure analysis, protein folding, hydrophobicity analysis (Girod A et al, 1999 supra)
  • the cap genes may according to preferred embodiments in addition have at least one further mutation being for example at least one point mutation, at least one internal deletion, insertion and/or substitution of one or several amino acids or at least one N- or C-terminal deletion, insertion and/or substitution of one or several amino acids, or a combination of these mutations, preferably a mutation inhibiting heparansulfate proteoglycan, integrins and/or Fibroblast Growth Factor Receptor (FGFR) binding.
  • FGFR Fibroblast Growth Factor Receptor
  • Such further mutations can be used for an additional modification of infectivity of the Cap protein/virion, for a reduction of an infection not mediated by AAV e.g. by reducing or abolishing binding for cellular receptors, or for a changed immu- nogenicity of the Cap protein/virion by reducing or abolishing the affinity to antibodies especially escaping from neutralizing antibodies.
  • cap genes may have a further constant insertion of at least one codon upstream and/or downstream of the insertion sites of the randomized nucleic acid sequences, preferably of one or two or three codons coding for Ala, Gly, Leu, He, Asp and/or Arg, especially an insertion of three Ala upstream and two Ala downstream of the insertion site.
  • this invention relates to a library of virions, especially parvovirus virions, with capsid protein modifications.
  • the library of virions contains parti- cles containing the genetic information necessary -to -generate viral progeny.
  • a preferred embodiment is a library of said virions, where each particle contains the genetic information necessary to generate viral progeny.
  • said library of virions is generated by using any of the above mentioned nucleic acids.
  • a further embodiment of this invention is a cap gene that comprises at least one recombination site within the cap gene, e.g. for the Gateway or cre/lox system, preferably after amino acid position 587 of VPl wherein the inserted nucleic acid sequences are inserted at any site within the first amino-terminal amino acids 1 to 50 of VPl, after corresponding amino acid positions 261, 381, 447, 534, 573, and/or 587 of VPl, preferably after amino acid position 447 or 587.
  • Especially preferred insertion sites are within the stretches consisting of amino acids (aa) i) aa 261-270, especially aa 269, ii) aa 324-331, iii) aa 380-383, especially aa 381, iv) aa 447-460, especially aa 447 and 451 -460, v) aa 484-503, preferably aa 484-499, especially aa 484, 487 or aa 494-499, vi) aa 507-514, especially aa 507, 509 or 514, vii) aa 527-534, especially 527-529, 532 or 534, viii) aa 548-556, ix) aa 572-575, especially 573, x) aa 581-595, especially 585, 587, 588 or 594.
  • the numbering of amino acids relates to the VPl protein of AAV2 (Girod A et
  • Stretches v) and vi) are especially preferred.
  • a further subject matter of this invention is a cap gene that comprises at least one recombination site within the cap gene, preferably for the Gateway or cre/lox system.
  • the recombination site may be inserted after a nucleic acid corresponding to any site within the first amino terminal amino acids 1 to 50 of VPl, or corresponding to amino acid positions 261, 381, 447, 534, 573, and/or 587 of VPl, preferably to amino acid position 447 or 587.
  • the numbering of the amino acids relates to the position within VPl.
  • corresponding sites of VP2 and VP3 of course have a different number.
  • This cap gene of the invention can be used as starting material for the method of the invention for producing a parvovirus library.
  • cap gene may comprise at least one endonuclease restriction site or polylinker that is not present in the respective wildtype gene site useful for the insertion at any site within the first amino-terminal amino acids 1 to 50 of VPl, after corresponding amino acid positions 261, 381, 447, 534, 573, and/or 587 of VPl, preferably after amino acid position 447 or 587.
  • the cap gene may comprise at least one endonuclease restriction site or polylinker that is not present in the respective wildtype gene.
  • the restriction site may be inserted after a nucleic acid corresponding to any site within the first amino-terminal amino acids 1 to 50 of VPl, or corresponding to amino acid positions 261, 381, 447, 534, 573, and/or 587 of VPl, preferably to amino acid position 447 or 587.
  • the endonuclease restriction site or polylinker may further contain a stop codon.
  • the cap gene of the invention may further have at least one mutation, preferably at least one point mutation, at least one internal deletion, insertion and/or substitution of one or several amino acids or at least one N- or C- terminal deletion, insertion and/or substitution of one or several amino acids, or a combination of these mutations.
  • such cap gene may have a further constant insertion of at least one codon upstream and/or downstream of the insertion sites of the randomized nucleic acid sequences, preferably of one or two or three codons coding for Ala, Gly, Leu, He, Asp and or Arg, especially an insertion of three Ala upstream and two Ala downstream of the insertion site.
  • the cap gene may contain non randomized codons for amino acid stretches of choice. This has the advantage that one can simultaneously screen for expressible structural genes with a wanted property by inserting a randomized insert and one or more further inserts at different sites to change the properties of such an expressible structural gene.
  • the invention can also be used to make or screen for vectors that have a reduced binding to antibodies (monoclonal or polyclonal antibodies/sera) and/or to have the ability to escape neutralizing antibodies and therefore are able to escape from an immune response in a patient.
  • the cap gene of the invention contains an insert with
  • a further subject matter of this invention is the nucleic acid encoding a cap gene with a sequence of the plasmid pWT99oen (Fig 1, sequence given and Example I)-
  • a further subject matter of this invention is a nucleic acid encoding a cap gene, wherein such cap gene has an insertion leading to additional amino acids com- prising an RGD or DDD motif, preferably an RGDXP or DDDXP motif, especially an RGD motif that is not present in human proteins, excluding the insertion AGTFALRGDNPQG.
  • Such cap gene may have the insertion corresponding to RGDXXXX, RGDXPXX, DDDXPXX, RGDAVGV or RGDTPTS, GKLFVDR, RDNAVVP, GENQARS, RSNGVVP, RSNAVVP or NSVRAPP.
  • the invention further ⁇ elates to Cap proteins encoded by the above- cap genes of the invention.
  • the inserted nucleic acid sequences may be inserted at any site corresponding to the first amino-terminal amino acids 1 to 50 of VPl, after corresponding amino acid positions 261, 381, 447, 534, 573, and/or 587 of VPl, preferably after amino acid position 447 or 587.
  • the nucleic acid of the invention may be inserted after a nucleic acid corresponding to any site within the first amino- terminal amino acids 1 to 50 of VPl, or corresponding to amino acid positions 261, 381, 447, 534, 573, and/or 587 of VPl, preferably to amino acid position 447 or 587.
  • the cap gene of the invention has at least one mutation leading to preferably at least one point mutation, at least one internal deletion, insertion and/or substitution of one or several amino acids or at least one N- or C- terminal deletion, insertion and/or substitution of one or several amino acids, or a combination of these mutations.
  • such cap gene may have a further constant insertion of at least one codon upstream and/or downstream of the insertion sites of the randomized nucleic acid sequences, preferably of one or two or three codons coding for Ala, Gly, Leu, He, Asp and/or Arg, especially an insertion of three Ala upstream and two Ala downstream of the insertion site.
  • the " invention further relates to ⁇ -he use of a nucleic acid of the invention encoding a cap gene for the preparation of a library of nucleic acids comprising a multiplicity of expressible cap genes from at least one eukaryotic virus, preferably a parvovirus.
  • inventions of this invention are vector constructs, bacteria or cells comprising any of the previously mentioned cap genes or constructs.
  • a vector construct comprising at least one nucleic acid from the library of the invention together with a second nucleic acid (especially packaging sequences such as AAV ITRs and one or more genes providing non-structural functions such as replication and packaging, for example functions of an AAV Rep protein) necessary for the packaging of a virion;
  • a second nucleic acid especially packaging sequences such as AAV ITRs and one or more genes providing non-structural functions such as replication and packaging, for example functions of an AAV Rep protein
  • steps iv) to vi) can be repeated several times.
  • the non-structural functions as for example the Rep protein can be provided in cis or in trans.
  • first cell and the second cell can be of the same kind or type.
  • a further embodiment of the invention is a method for the selection of a recombi- nant virion with an increased infectivity or specificity for a specific cell type, that at the same time has a reduced or no infectivity for another cell type.
  • the above method additionally comprises the steps
  • virions that are able to infect such third cells enter the cells but do not replicate within these cells due to the non-permissiveness of the cells. Therefore such virions are depleted from the library. Also these steps can be repeated on the same or different cell types.
  • Non-permissive cells can be obtained for both helper dependent and helper independent virions by not providing such third cell with all necessary cellular, viral, physical and/or chemical functions for the packaging of virions.
  • drugs that inhibit viral replication and/or packaging but not infection such as acilovir for HSV.
  • this invention relates to a method for the identification of a mutant cap gene leading to virions having an increased infectivity or specificity for a specific cell type comprising the previous steps and in addition the step of cloning the nucleic acid of the cap gene(s) of the virion.
  • the method for selection of a recombinant virion invention further includes a step for the additional selection of virions, preferably an affinity binding step of virions (e.g. to a known receptor or binding motif that may be coupled to beads or a resin, for example by an affinity chromatography), an ion exchange chromatography step (to improve purifaction capabilities of such virions) or an immuno-selection step (to circumvent potential immune reactions from patients, e.g. by immuno depletion with antibodies).
  • an affinity binding step of virions e.g. to a known receptor or binding motif that may be coupled to beads or a resin, for example by an affinity chromatography
  • an ion exchange chromatography step to improve purifaction capabilities of such virions
  • an immuno-selection step to circumvent potential immune reactions from patients, e.g. by immuno depletion with antibodies.
  • the invention relates to a method for the selection of a receptor binding motif comprising the steps as defined above, wherein such second cell is permissive for the respective vector.
  • Such receptor may be expressed recombinantly, preferably over-expressed by known recombinant technologies.
  • a further embodiment of the invention is a method for the in vivo selection of a recombinant virion capable of infecting a specific cell type comprising the steps of (i) providing at least one first cell with a vector construct comprising at least one nucleic acid from the previously described library together with packaging sequences such as AAV ITRs and one or more genes providing necessary non-structural functions such as replication and packaging, for ex- ample of an AAV Rep protein for the packaging of a virion;
  • This method can be used for the identification of a mutant cap gene leading to virions having an increased infectivity or specificity for a specific cell type by addition of the step of cloning the nucleic acid of the cap gene(s) from such cell type of the animal.
  • a second nucleic acid especially sequences such as AAV ITRs and one or more genes providing non-structural functions such as replication and packaging, for example functions of an AAV Rep protein
  • steps iv) to vii) can be repeated several times.
  • the non-structural functions as for example the Rep protein can be provided in cis or in trans.
  • first and the second cell can be of the same kind or type.
  • the immunoselection steps are well known in the art.
  • monoclonal or polyclonal antibodies For example one can pre-incubate the produced virions with monoclonal or polyclonal antibodies. If antibodies bind to a critical site of the virion that is involved in the mechanism of infection, this will result in a negative selection for virions recog- nized by such antibody.
  • the polyclonal antibod- ies contained in this sera would have the advantage, that one can negatively select for virions that escape neutralizing antibodies without having the antibody isolated.
  • a further immunoselection step of choice is an immunodepletion reaction using affinity chromatography with antibody columns.
  • Column material such as CNBr-activated Sepharose can be used to bind -monoclonal or polyclonal antibodies.
  • Produced virions can then be incubated with such antibody column leading to an eluate of the column where binding virions have been depleted.
  • the invention further relates to a polypeptide comprising a peptide with the se- quence RGDAVGV, RGDTPTS, GKLFVDR, RDNAVVP, GENQARS, RSNGVVP, RSNAVVP or NSVRAPP.
  • the polypeptide of the invention consists of a peptide with the sequence RGDAVGV, RGDTPTS, GKLFVDR, RDNAVVP, GENQARS, RSNGVVP, RSNAVVP or NS VRAPP.
  • the polypeptide of the invention is a Cap polypeptide, preferably derived from a parvovirus, especially from an AAV.
  • the invention further relates to the use of a polypeptide as defined above or comprising or consisting of a peptide with the sequence RGDXXXX, RGDXPXX, or DDDXPXX with the exception of AGTFALRGDNPQG, for the retargeting of eukaryotic viruses, preferably parvorviruses, especially AAV.
  • all identified peptides can be used for the targeting of non-viral vectors.
  • Other potential uses of the peptides are triggering or blocking cellular pathways e.g. by the activation or inhibition of the receptor due to the binding of isolated peptides to the respective receptor.
  • the peptides also can be used as fusions with other peptides or any other suitable molecules of choice.
  • the peptides in this setting can be used to couple such fusion to the surface of a cell for the purpose of - for example - staining, tagging, sorting or killing of the cell.
  • the peptides can also be used for the purification of fusions or virions containing them by coupling the respective receptor onto beads and allowing binding of such fuions/virions to such coupled beads (affinity chromatography). Therefore such selected virions not only have the advantage of a changed cell specificity but also that they can be purified by affinity chromatography using their specific receptor.
  • RGDAVGV and RGDTPTS as well as RGDXXXX, RGDXPXX and DDDXPXX are useful in combination with cells that express RGD binding intergrins.
  • RGD binding integrins are receptors that are widely expressed among eukaryotic cells (Ruoslahti E (1996) Annual Review of Cell and Developmental Biology 12, 697-715; Aumailley M et al. (1990): FEBS Lett 12:262(l):82-6).
  • An example for an integrin that binds RGD motifs are the ⁇ v ⁇ 5 and the ⁇ integrins.
  • Such cells are for example megakaryocytes, e.g. the cell line used for the screen- ing M-07e.
  • the peptides GKLFVDR, RDNAVVP, GENQARS, RSNGVVP, RSNAVVP or NSVRAPP are useful for B-CLL cells and Mecl cells. These peptides bind to one or more cellular receptors that have not been identified so far. Every cell or cell line that expresses one or more of these receptors is a potential target for these peptides. It is known in the art how to test a cell or cell line, if one of the peptides is capable of binding to the cell surface. Since these peptides were identified by screening the library against hematopoetic cells, it is reasonable to predict that many other hematopoetic cells will bind those peptides, for example B cells.
  • the invention further relates to a recombinant virion obtainable by the methods of the invention for the selection of a recombinant virion.
  • the invention relates to a mutant cap gene obtainable by the methods of the invention for the identification of a mutant cap gene. Furthermore, the invention relates to a Cap protein encoded by the mutant cap gene of the invention.
  • the invention relates to a virion comprising the Cap protein of the invention.
  • the invention relates to a medicament for the treatment of a patient suffering from cancer, an autoimmune disesase, an infectious disease or a genetic defect comprising a virion, a cap gene or a Cap protein of the invention.
  • the invention relates to a method for treating a patient suffering from cancer, an autoimmune disesase, an infectious disease or a genetic defect comprising administering to the patient a virion, a cap gene, or a Cap protein of the invention.
  • FIG. 1 Schematic map of the plasmid pwt99oen.
  • FIG. 2 Construction of the library of AAV-2 capsid modified particles.
  • a pool of randomly generated oligonucleotides was cloned in an AAV-2 genome encoding plasmid at the site corresponding to amino acidic site 587 of capsid protein VPl.
  • the obtained pool of plasmids was transfected into 293 cells.
  • a library of approximately 10 capsid modified AAV-2 clones was generated.
  • Fig. 3 AAV display screening procedure for the selection of retargeted mutants.
  • Target cells were infected with the library of capsid modified AAV-2 clones and with adeno virus (helper for AAV replication). Non infectious virions are removed by washing steps 2h post infection. The viral progeny collected 48h p.i. was used for the next selection round. The evolution of the AAV population after each round was monitored by titer determination and sequencing.
  • Fig. 4 Example of evolution of the viral population during 6 selection rounds on M07e cells.
  • A Dot blot assay quantification of viral progeny harvested after each infection cycle.
  • B Sequencing of the random insertion containing region of the cap gene shows the progressive loss of heterogenity in the viral population collected after each selection round. After 5 rounds a single clone (in the shown example carrying a RGDAVGV inserted sequence) could be detected in the viral progeny.
  • Transduction efficiencies ⁇ standard deviation as determined by FACS analysis in duplicate experiments for selected rAAV-GFP mutants (black bars). Transduction rates were also assessed after pre-incubation of viral preparation with soluble heparin (white bars) or pre-incubation of the cells wi h competing GRGDTP (gray bars) and inactive GRGES peptides (checked bars).
  • Fig. 6 A neutralization assay on HeLa cells.
  • A Neutralizing antibody titers against rAAV and rAAV-587/L14. Serial dilutions (1 :10 - 1 :1200) of 15 neutralizing human serum samples (P3 - P65) were analyzed on HeLa cells. As control, rabbit serum directed against the inserted L14-ligand ( -L14) was tested. The neutralizing titers (N 50 ) are expressed as the dilution at which transduction was 50% reduced compared to the positive control.
  • rAAV (B) and rAAV-587/L14 (C) were incubated with serum P35 (1 :80) prior infection of HeLa cells. GFP expression was monitored by fluorescence microscopy 48 hours post infection.
  • Fig. 7 A neutralization assay on B16F10 cells. Infection of irradiated B16F10 cells with rAAV-587/L14 alone (A) or after co-incubation with P35 serum (C) or anti-L14 serum (D) at a 1:80 serum dilution. Cells were analyzed for GFP expression by fluorescence microscopy after 72 hours.
  • Fig. 8 The effect of neutralizing antisera on rAAV-587/MecA transduction.
  • Genomic titers were measured by dot blot assay. Infectivity of the mutants for Hela, M07e and Mecl cells was measured by FACS analysis after infecting the cells with identical genomic particles/cell ratios. For each cell line, the transduction rate was normalized to 100% for the mutant corresponding to bold values. The ability of soluble heparin to inhibit infection of Hela cells was assessed preincubating viral preparations with soluble heparin.
  • plasmid pWtoen For the construction of plasmid pWtoen, the HCMV promoter/enhancer cassette and the GFP open reading frame in the plasmid pEGFPC-1 (Clontech, Palo Alto, California) were substituted with the wt AAV-2 genome encoding fragment of plasmid pUC-AV2 (Girod A et al (1999) supra). A DNA fragment encoding amino acids AAAstopA and the restriction sites Notl and Ascl was inserted between amino acid position 587 and 588 by PCR mutagenesis. To generate a library of AAV plasmids (p587Lib7) a pool of single strand DNA molecules was synthesized as
  • Plasmids pRC, pXX6 (obtained from J. Samul- ski, Chapel Hill, North Carolina) and psub/CEP4/EGFP were previously de- scribed (Girod A et al (1999) supra, Xiao X et al (1998) J. Virol. 72, 2224-32).
  • pRC, pXX6 obtained from J. Samul- ski, Chapel Hill, North Carolina
  • psub/CEP4/EGFP were previously de- scribed (Girod A et al (1999) supra, Xiao X et al (1998) J. Virol. 72, 2224-32).
  • 15 150 mm Petri-dishes of 293 cells at 80% confluence were co-transfected with 37.5 ⁇ g of DNA.
  • p587Lib7 and plasmid pXX6 were co-transfected at a molar ratio of 1:1.
  • rAAV-wt For the production of rAAV-wt, the cells were co-transfected with vector plasmid psub/CEP4/EGFP, packaging- plasmid pRC and adenoviral plasmid pXX6 at a molar ratio of 1 :1:1.
  • pRC plasmids modified to contain the appropriate Notl-Ascl retargeting insertion were used.
  • LI 4- AAV was produced using plasmid pI-587 instead of pRC (Girod A. et al supra). After 48 hrs cells were collected and pelleted by centrifugation.
  • HeLa cells human cervix epitheloid carcinoma, ATCC CCL 2
  • M-07e cells a human megakaryocytic leukemia cell line (obtained from James D. Griffin, Boston, Massachussets), Mecl, a cell line derived from a patient with B-CLL in pro- lymphocytoid transformation (obtained from Federico Caligaris-Cappio, Torino, Italy), CO-115 cells (human colon carcinoma), and 293 cells (human embryonal kidney) were maintained in Dulbecco's modified Eagle's medium (DMEM) (HeLa and 293), DMEM/NUT.Mix.F-12 medium (CO-115), RPMI medium (M-07e) or Isocove's medium (Mecl) supplemented with 10% fetal calf serum (FCS), penicillin (100 U/ml) and streptomycin (100 ⁇ g/ml), and L-glutamine (2 mM), at 37 °C and
  • IL-3 interleukin 3
  • Peripheral blood was obtained with informed consent from four patients with an established diagnosis of B-CLL.
  • Mononuclear cells were isolated on a Fi- coll Hypaque (Seromed, Berlin, Germany) density gradient by centrifugation, depleted of monocytes by adherence to plastic tissue culture flasks and cultivated in Isocove's medium supplemented as for Mecl cells. More than 98% of isolated cells co-expressed CD5 and CD 19 as assessed by flow cytometry, therefore non- malignant B cells did not constitute a meaningful fraction of the total cells isolated. Patients were either untreated or had not received cytoreductive treatment for a period of at least one month before investigation and were clinically stable and free from infectious complications.
  • Cells were seeded in 96 or 24 well plates (Nunc, Wiesbaden, Germany) and infected with rAAV-GFP clones, harvested 48 hrs p.i., washed and resuspended in 1 ml PBS. The percentage of GFP expressing cells was determined by flow cytometry with a Coulter Epics XL-MCL (Beckman Coulter, Krefeld, Germany). A minimum of 5000 cells were analyzed for each sample.
  • Infectivity of the retargeted mutants was determined in the presence or absence of various concentrations of GRGDTP or GRGES peptides (Bachem, Bubendorf, Swiss) or 5 I.U./ ⁇ l soluble heparin (Braun, Melsungen, Germany).
  • target cells were super-infected with 1000 genomic library particles/cell and with adenovirus at an MOI of 20 and incubated at 37°C. 2 hrs p.i. cells were cen- trifuged, resuspended in fresh culture medium and incubated at 37°C. 48 hrs p.i., cells were rinsed with 5 ml PBS, resuspended in 5 ml of lysis buffer (150 mM NaCI, 50 mM Tris/HCI, pH 8.5) and lysed through 3 freeze/thaw cycles. Cellular debris was removed by centrifugation and the supernatant was used to infect the next batch of target cells (second round of infection).
  • lysis buffer 150 mM NaCI, 50 mM Tris/HCI, pH 8.5
  • Example 2 Selection of AAV-2 retargeted mutants for M-07e and Mecl cells
  • the potential of the AAV display system for the generation of retargeted mutants was tested on two cell lines that are resistant to wt AAV-2 infection.
  • M-07e is a human megakaryocytic cell line (Avanzi GC et al (1988) Br. J. Hae- matol. 69, 359-66). Failure of AAV-2 to infect these cells has justified the use of this cell line as negative control in several reported AAV-2 infection experiments Bartlett JS et al. (1999) Nat. Biotechnol. 17, 181-186; Ponnazhagan S et al (1996) J. Gen. Virol. 77, 1111-22).
  • Mecl is a cell line derived from B-cell chronic lymphocytic leukemia (B-CLL) cells in prolymphoid transformation (Stacchini A et al. (1999) Leuk. Res. 23, 127- 36) and is also resistant to wt AAV-2 infection.
  • B-CLL B-cell chronic lymphocytic leukemia
  • Fig. 4 A typical selection is depicted in Fig. 4.
  • the amount of viral DNA detected in the crude lysates and the analysis of the sequence showed that the number of recovered virions increased after each round, while the heterogeneity of the pool was progressively lost. After 5 rounds only one single clone was present in the viral progeny.
  • Application of the library to M-07e cells led to the selection of a clone carrying an RGDAVGV sequence at the 587 site (Fig.
  • the selected DNA sequences were cloned into appropriate plasmids for the production of capsid-modified recombinant AAV (rAAV) vectors encoding the enhanced Green Fluorescent Protein (GFP).
  • rAAV capsid-modified recombinant AAV
  • GFP Green Fluorescent Protein
  • rAAV-M07A RGDAVGV insertion
  • rAAV-M07T RGDTPTS insertion
  • rAAV-MecA GFP-expressing retar- geted vectors rAAV-M07A (RGDAVGV insertion), rAAV-M07T (RGDTPTS insertion), rAAV-MecA (GENQARS insertion) and rAAV-MecB (RSNAVVP insertion) were produced (see Example 1) and genomic titers were determined by dot blot assay. Genomic titers of the selected mutants were comparable or higher than titers of AAV vector
  • the selected capsid mutants were tested for their ability to transduce M-07e cells (Fig. 5a).
  • the mutants rAAV-M07A and rAAV-M07T transduced 50 ⁇ 2.5% and 47 ⁇ 2.7% of M-07e cells, respectively, representing a 100 and 94 fold increase in comparison to rAAV-wt transduction efficiency (0.5 ⁇ 0.01%).
  • rAAV-MecA and rAAV-MecB transduced M-07e cells with an efficiency of only 8.1 ⁇ 1.5% and 16 ⁇ 2%.
  • the transduction efficiency of the virus mutants rAAV-M07A, rAAV-"M07T, rAAV-MecA and rAAV-MecB was reduced by 50, 43, 12 and 31%, respectively, when compared to wt AAV-2 (Fig. 5c), while it was similar to wt AAV-2 in HeLa cells (Fig. 5d).
  • transduction by mutants rAAV-M07A and rAAV-M07T was blocked almost completely by the GRGDTP peptide, but not by the GRGES peptide nor by hepa- rin.
  • Fig. 5e Successful retargeting of mutants selected on Mecl cells is depicted in Fig. 5e. While transduction of Mecl cells by rAAV-wt was not detectable, mutants rAAV- MecA and rAAV-MecB transduced up to 23% of these cells at a genomic particle/cell ratio of 4x10 4 . Using rAAV-MecA, we then examined the transduction efficiency in primary leukemia cells in order to explore the potential clinical rele- vance of the AAV display technology.
  • Primary B-CLL cells are resistant to transduction by most currently available vital vector systems, including AAV (Cant- well MJ et al (1996) Blood 88, 4676-83; Rohr UP et al (1999) Blood 94, 181a).
  • AAV Cant- well MJ et al (1996) Blood 88, 4676-83; Rohr UP et al (1999) Blood 94, 181a).
  • rAAV-MecA (8xl0 4 genomic particles/cell) transduced primary leukemia cells isolated from four B-CLL patients at an efficiency of 54, 49, 23 and 21%, respectively (Fig. 5f).
  • rAAV-M07A and rAAV-M07T failed to transduce primary B-CLL cells (data not shown).
  • An additional upgrade of this technology might be the generation of an AAV library with randomized insertions in multiple sites of the capsid.
  • the virus display might be also used for the identification of capsid variants that are less efficiently recognized by human antibodies or immune effector cells.
  • the shortness of the insertions that were successfully used to generate retargeting clones suggests that this technology might be applicable in other viral systems.
  • a combinatorial library of AAV for the selection of retargeted clones was generated by cloning randomly generated oli- gonucleotides with a length of 21 bases at the genomic site corresponding to aa position 587 using the plasmid pWT99oen (Fig. 1, sequence given).
  • This pool of plasmids was transfected into 293 packaging cells concomitantly to a helper plasmid containing the genes of adenovirus, necessary for the packaging of AAV virions.
  • Viral progeny was harvested by a standard purification protocol on an iodixanol discontinuous gradient (Samulski et al.).
  • Genomic and infectious titers of the viral preparation were measured by dot blot and immunofluorescence analysis using an anti rep antibody and quantified in respectively 4xlO n virions/ml and 6xl0 8 /ml.
  • Fig. 4 The sequence obtained after digestion of viral proteins with ProteinaseK and phenol/chloroform extraction is depicted in Fig. 4 and confirms the randomized nature of the insertion at the 587 site.
  • the culture medium was changed to remove non-infectious mutants.
  • 48 hours p.i. cells were centrifuged, rinsed with PBS, resuspended in 5 ml lysis buffer and subjected to 3 freeze/thaw cycles to allow diffusion of the progeny virions into the solution. Cellular debris was separated by centrifugation at 5000 g.
  • the M07e cell line is resistant to wt AAV-2 infection. This characteristic has been attributed to the lack of expression of the putative primary receptor for AAV-2 (heparan sulfate proteoglycan), and has justified the use of this cell line as negative control in many reported AAV-2 infection experiments.
  • Fig. 4 shows the results of 5 rounds of infection/harvesting of the AAV pool on this target cells. Round after round, we could observe a slight increase of the AAV genomic titer in the crude lysates preparation (as assessed by dot blot analysis). Concomitantly, the peaks of the sequence-reaction chart in the random insertion portion became increasingly higher during the selection procedure, and at the 5 th cycle it was possible to read a fixed sequence from the sequencing reaction. The selection procedure was performed in two independent experiments and resulted in the identification of two DNA sequences encoding for respectively RGDAVGV and RGDTPTS peptides. Figure 4 depicts only the experiment that generated he RGDAVGV sequence.
  • the selected DNA sequences were cloned into appropriate plasmids for the production of capsid-modified recombinant AAV vectors encoding for the Enhanced Green Fluoresent Protein (rAAV-GFP).
  • GFP expressing versions of these retar- geted clones (rAAV-M07A containing the RGDAVGV sequence and rAAV- M07T containing the RGDTPTS sequence) were produced by standard rAAV production protocols.
  • mutants rAAV-M07A and rAAV-M07T were compared with the efficiencies of vectors with unmodified capsid (rAAV-wt) and of vectors expressing the L14 sequence at the 587 site (rAAV-L14).
  • M07e cells were infected with identical genomic particles/cell ratios (Fig. 5). Transduction rates were higher than 88% when using the retargeted mutants, 6% using unmodified capsid mutants and 18% using rAAV-L14.
  • rAAV-L14 carries a RGD motif containing sequence (of the laminin fragment PI) inserted at the 587 site.
  • RGD motif containing sequence of the laminin fragment PI
  • Mecl is a cell line derived from B-Cell Chronic Lymphocytic Leukemia cells in prolymphoid transformation (Stacchini et al.) and is resistant to wt AAV-2 infec- tion.
  • the GENQARS sequence was cloned into an appropriate plasmid for the production of capsid-modified recombinant AAV vectors encoding for the Enhanced Green Fluoresent Protein (rAAV-GFP). GFP expressing viral particles of this retargeted clone (rAAV-Mecl) were produced by standard rAAV production protocols.
  • a detailed understanding of major immunogenic domains on the adeno-associated virus (AAV) capsid is not only important with regard to the binding of serum an- tibodies to the virus and its subsequent neutralization by the immune system, but also with regard to the existence of neutralizing antibodies that directly inhibit infection of the target cells by AAV vectors.
  • AAV vector coding for GFP and carrying the L 14 ligand at position 587 (rAAV-587/L14) to determine whether this modification would block the neutralizing ability of human antisera.
  • transduction by rAAV-587/L14 was 8 up to 64 fold less reduced than transduction by rAAV (mean 15 fold).
  • transduction by rAAV- 587/L14 was only slightly impaired, with neutralizing titers of 1 :80 or lower, demonstrating the ability of rAAV-587/L14 to escape the effects of neutralizing Ab (Fig. 6A).
  • rAAV-587/L14 was able to escape the neutralizing Ab in serum P47 at any dilution tested, and serum samples PI 7, P31 and P37 reduced transduction only at a dilution of 1 :20, where unspecific interactions could not be excluded.
  • FIGS. 6B and 6C show one representative experiment with serum P35, which completely inhibited transduction by rAAV at a 1:80 dilution (Fig. 6B). In marked contrast, transduction by rAAV-587/L14 was not affected (Fig. 6C). Only two serum samples (PI 6 and P48) were able to neutralize rAAV- 587/L14 transduction efficiently, with a N50 of 1:320. We assume that this was due to the high neutralizing Ab content in these serum samples, because transduction by rAAV-587/L14 still remained less affected than transduction by rAAV. As an additional control, the monoclonal Ab C37-B was tested.
  • C37-B is a neutralizing Ab that inhibits binding of AAV to the host cell (Wobus CE et al. supra). It failed to bind rAAV-587/L14 in an ELISA (data not shown), therefore it should not interfere with rAAV-587/L14 transduction. As expected, rAAV-587/L14 transduction was not neutralized by C37-B, while -rAAV transduction could be totally inhibited by this antibody (data not shown). In marked contrast, anti-L14 serum, which was generated against the L14 ligand, neutralized rAAV-587/L14 transduction completely at a 1:160 dilution, while rAAV transduction remained unaffected (Fig. 6A).
  • rAAV-587/MecA that carries a 7 aa ligand (GENQARS) at position 587.
  • This mutant has been selected by AAV- display on Mecl cells and efficiently transduces Mecl cells and primary B-cells from chronic lymphocytic leukemia patients in a receptor specific manner (as described before).
  • rAAV-587/MecA and rAAV were incubated with the serum P35 before Mecl cells were infected. Transduction of Mecl cells by rAAV-587/MecA was not affected by the neutralizing Ab of serum P35 (1 :80 dilution).
  • Another possibility to increase specificity of the vectors is the introduction of subtractive selection rounds, e.g. infecting cells for which the infection is unde- sired and recovering the non-infectious virions containing supernatant, or using affinity columns to deplete the viral population from column-binding clones.
  • subtractive selection rounds e.g. infecting cells for which the infection is unde- sired and recovering the non-infectious virions containing supernatant, or using affinity columns to deplete the viral population from column-binding clones.
  • a further upgrade of the system that is underway in our lab is the generation of an AAV library with randomized insertions at the level of multiple capsid protein sites.
  • the technology described herein for the adeno-associated virus can be adapted for any viral system.
  • the AAV display will be a valuable tool for the understanding of the biology of this virus, for the characterization of peptides with interesting biological properties, and for the investigation of specific ligand-receptor interactions.

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Abstract

Cette invention porte sur une bibliothèque d'acides nucléiques comprenant une multiplicité de gènes structuraux pouvant être exprimés, de préférence des gènes cap, issus d'un virus eucaryotique, de préférence un parvovirus.
PCT/EP2002/014750 2001-12-21 2002-12-23 Bibliotheque de genes structuraux modifies ou de particules modifiees par des capsides utiles pour l'identification de clones viraux par tropisme cellulaire desire Ceased WO2003054197A2 (fr)

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ES02787962.6T ES2467156T3 (es) 2001-12-21 2002-12-23 Una biblioteca de genes estructurales modificados o de partículas modificadas de cápside útiles para la identificación de clones virales con tropismo celular deseado
US10/498,163 US20050106558A1 (en) 2001-12-21 2002-12-23 Library of modified structural genes or capsid modified particles useful for the identification of viral clones with desired cell tropism
EP02787962.6A EP1456383B1 (fr) 2001-12-21 2002-12-23 Bibliotheque de genes structuraux modifies ou de particules modifiees par des capsides utiles pour l'identification de clones viraux par tropisme cellulaire desire
CA2468882A CA2468882C (fr) 2001-12-21 2002-12-23 Bibliotheque de genes structuraux modifies ou de particules modifiees par des capsides utiles pour l'identification de clones viraux par tropisme cellulaire desire
JP2003554898A JP2005512569A (ja) 2001-12-21 2002-12-23 目的とする細胞指向性をもつウイルスクローンの同定に有用な修飾した構造遺伝子またはキャプシド修飾した粒子のライブラリー
AU2002352261A AU2002352261B2 (en) 2001-12-21 2002-12-23 A library of modified structural genes or capsid modified particles useful for the identification of viral clones with desired cell tropism

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WO2025102034A1 (fr) 2023-11-10 2025-05-15 The Trustees Of The University Of Pennsylvania Thérapie génique pour le syndrome de barth
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EP1486567A1 (fr) * 2003-06-11 2004-12-15 Deutsches Krebsforschungszentrum Stiftung des öffentlichen Rechts Vecteur derivé d'un virus associé aux adenovirus pour la thérapie génique
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AU2002352261B2 (en) 2008-02-07
EP1456383B1 (fr) 2014-03-12
CA2468882A1 (fr) 2003-07-03
ES2467156T3 (es) 2014-06-12
CA2468882C (fr) 2015-09-29
AU2002352261A1 (en) 2003-07-09
EP1456383A2 (fr) 2004-09-15
EP2363487A3 (fr) 2012-03-21
WO2003054197A3 (fr) 2004-03-18
AU2008202032B2 (en) 2012-09-20
JP2005512569A (ja) 2005-05-12
EP2363487A2 (fr) 2011-09-07
AU2008202032A1 (en) 2009-11-26
US20050106558A1 (en) 2005-05-19

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